Sue Lynch

Principal Investigator

Dr. Lynch is an Associate Professor of Medicine, at the University of California San Francisco, where she also Directs the Microbiome Research Core and acts as Associate Director of the Microbiome in Inflammatory Disease Program. Dr. Lynch graduated from University College Dublin and completed her postdoctoral studies at Stanford University. Her laboratory is located in the Division of Gastroenterology, at the University of California san Francisco, Parnassus Campus.  



Dr. Lynch is an Associate Professor of Medicine, at the University of California San Francisco, where she also Directs the Microbiome Research Core and acts as Associate Director of the Microbiome in Inflammatory Disease Program. Dr. Lynch graduated from University College Dublin and completed her postdoctoral studies at Stanford University. Her laboratory is located in the Division of Gastroenterology, at the University of California san Francisco, Parnassus Campus.  


Post-doctoral Scholars

Julia Durack, Ph.D. 

Julia received her Ph.D. in 2010 from University of Tasmania, Australia, where she succeeded in characterizing the physiological response to stress, utilized in the food industry to preserve goods for human consumption, in multiple strains of food-born pathogen Listeria monocytogenes. She began her postdoctoral studies in laboratory of Dr. Daniel Portnoy (2012-2013) in the Department of Molecular and Cell Biology, University of California Berkeley on elucidating the function of the accessory cytosolic motor protein SecA2 in aiding intracellular virulence of L. monocytogenes. In 2013, she joined the Lynch Lab where her primary research focus is aimed at understanding the contribution of the airway and gastrointestinal microbiota to pathogenesis of asthma.



Nikole Kimes, Ph.D.

Nikole, a former NSF Graduate Research Fellow (2007-2010), completed her Ph.D. in the lab of Pamela J. Morris at the Medical University of South Carolina. She then moved to Alicante, Spain to perform postdoctoral research at the Universidad Miguel Hernández with Francisco Rodriguez-Valera (2012-2014). Her interest in molecular and genomic microbiology focused on marine microbial communities associated with corals, deep-sea sediments, dolphins and the Mediterranean Sea. Utilizing genomic and metagenomic sequencing, coupled with more traditional phenotypic and physiological techniques, she investigated the ecological impact of individual community members, interactions between different community members, and community function as a whole. In the Lynch lab (2014-2016), she combined her experience in marine microbial systems with her interest in human health to further elucidate the influence of microbial communities in human health and disease, developing a therapeutic microbial consortium that alleviates allergic airway inflammation in a murine model.


Graduate Students

Sophia Levan, B.A.

Sophia Levan is a MD/PhD Candidate and completed her B.A. at Wesleyan University where she majored in Chemistry and Molecular Biology with a concentration in Biophysics. Following her B.A., Sophia completed a year-long post-bac at the National Institute on Aging. She joined the MSTP at UCSF in 2013. Sophia’s research interests include host-microbe interactions, human immune development, and the early-life microbiome.



Sandra Ovesen

Sandra is a visiting research scholar at the Lynch Lab. She is a medical grad student from Aalborg University in Denmark. During her one year research fellowship she will investigate the virulent properties of the enteric pathogen Campylobacter concisus and its relation to Inflammatory Bowel Diseases(IBD). She will determine the relative abundance of C. concisus in patients with gastroenteritis and IBD and investigate the gut microbial communities of C. concisus infected patients. 



Ariane Panzer, B.A.

Ariane is from Austin, TX. We secretly hope that Texas will secede some day, but considering the dismal results of the elections, Texas can stay and California will leave. Yes, she has a Siamese twin (Ariel) who unfortunately for her is not in grad school, has no interest in biomedical research and is forced to tag along.  Sadly for Ariel no one takes her seriously after her parents admitted naming her after Disney's Little Mermaid. Ariane and Ariel went to some small liberal arts school back East. 



Elze Rackaityte, B.A.

Elze graduated Wellesley College with a BA in Biological Sciences. She then trained at Institut Pasteur in a bacterial biofilm laboratory. Currently, she is a graduate student in Biomedical Sciences program at UCSF. Her project investigates the convergence of microbiome and immune development in early life. In her free time, she enjoys various fermented goods. 



Meera Shenoy, B.S.

Meera completed her B.S. in Microbiology at the University of Washington in 2013, where she identified a single nucleotide polymorphism that regulates expression of the CD1A gene and is associated with active Mycobacterium tuberculosis infection. She also worked on the development of functional gold nanoprobes that assemble intracellularly for targeted bioimaging. Prior to her undergraduate work, she interned at Philips Medical Systems, where she examined the efficacy of CPR versus immediate AED shocks during cardiac arrest. Currently she is a PhD candidate in the Biomedical Sciences Program at UCSF. Her project focuses on the relationship between airway and gut networks of microbial co-association within HIV-infected patients who contract acute pneumonia, and the role of these microbial networks in shaping host immune and metabolic response. In her free time, she enjoys blatantly ignoring protocols, i.e. recipes, while cooking.



Germaine Yong, B.S.

Germaine completed her undergraduate studies in Biology at Duke University in 2014, where she investigated the role of microbial communities in marine biofouling. After graduation, she developed a method to measure in vivo growth rates of Candida albicans under the mentorship of Norman Pavelka at the Singapore Immunology Network. She also worked with Chong Yap Seng and Lynette Shek at the Singapore Institute of Clinical Sciences, where she investigated how polyunsaturated fatty acids influenced risk of infections in infants from the Growing Up in Singapore Towards Health Outcomes (GUSTO) birth cohort. Germaine joined the Lynch lab in 2016 as a UCSF Biomedical Sciences graduate student. She currently studies the role of the early life gut microbiome in the development of childhood obesity, and is interested in using early life nutrition as an effective strategy to alleviate metabolic dysfunction.



Doug Fadrosh, M.S. Lab Manager

If you have any questions or complaints please direct them all to Doug. He will answer everything. He especially likes answering questions about general departmental GI information. Doug is an avid Oakland Raiders fan and would appreciate anyone sending him Raider gear and paraphernalia. His child looks amazing in Black & Silver.  Doug is a cross between Tyrion Lannister and Ramsey Bolton, but we call him Drogon.



Kei Fujimura, Ph.D.

Kei completed her Ph.D. at the University of Northern British Columbia in Keith Egger's lab examining the effects of climate change on root-associated fungal communities in the Canadian High Arctic (Ellesmere Island). She joined the Lynch Lab in 2008 as a post-doc transferring her microbial ecology skills from fungal to bacterial communities. She focusses on environmental and gut microbiomes and how they are associated with allergy and asthma development in children, working on the MAAP (Microbes, Allergy, Asthma and Pets) and URECA (Urban Environment and Childhood Asthma) studies.



Brandon LaMere, M.Ph.

Brandon is from somewhere in cold Michigan and move to California to warm up.  He's often the most stylish in group (after Sue) and enjoys collecting poo. Brandon is a cross between Wun Wun and the 3-eyed Raven and is secretly  glad that winter is coming so that he doesn't have to go back to Michigan.


    Din Lin, Ph.D.

Din is the key immunologist of the group. He development an ex vivo  assay to test the host immune response  to bacterial communities and metabolites. He previously worked in the McCune lab examining if the induction of specific tolerance to SIV in utero and/or orally at birth has an impact on the course of SIV infection after birth in Rhesus macaques, and investigate the response of immunomodulatory drugs in SIV-infected Rhesus macaques. He is currently examining the immune modulatory and epigenetics regulatory response to commensal microbial agents in both humans and mice.



Kole Lynch, B.S.

As a Research Associate in the Lynch lab, Kole supports the 16S rRNA sequencing Core where he manages sample processing from DNA extraction all the way to NextGen sequencing. More recently, He has been expanding his skill set by using a microbial consortium to investigate chronic allergic disease in the gut. Kole is originally from Gardnerville, Nevada and grew up skiing the Sierras, camping in the Nevada high desert, and fishing the Truckee River. After completing his high school education as a homeschool student, he attended the University of Nevada, Reno where he completed a dual Bachelor’s of Science in Biochemistry and Microbiology. After graduation, he found himself relocating to the Bay Area to further pursue his goal of applying to medical school. In the near future, Kole plans to study neurodegenerative disease and how the human microbiome influences the onset of synucleinopathies. 


Katie McCauley, MPH

Katie received her Masters of Public Health degree in Epidemiology/Biostatistics from UC Berkeley, where she focused on international, multi-center studies of childhood leukemia etiology.  She became fascinated by the microbiome through her MPH coursework, and joined the Lynch Lab in February 2016. Her work now focuses primarily on longitudinal analyses of airway microbiota from children of diverse backgrounds. Katie also provides occasional statistical guidance for other projects throughout the group.





Yvette M. Piceno, Ph.D.

Yvette obtained her doctoral degree in Biology, having studied the distribution of nitrogen-fixing bacteria in saltmarsh cordgrass rhizospheres along a tidal gradient and the response of the diazotrophs to altering plant resource allocation. She then joined Microbial Insights, Inc., a company specializing in microbial community profiling using molecular techniques, primarily focused within the environmental/bioremediation field. There she lead research for product and market development, as well as directed the molecular facilities. In 2004, Dr. Piceno joined Dr. Gary Andersen’s lab at the Lawrence Berkeley National Laboratory, working on numerous collaborative studies, ranging from ocean systems, oil reservoirs, and rock or agricultural soils, to human gut microbiome studies for chronic kidney disease patients. Yvette recently joined the Lynch Lab (July 2016) and will apply high-throughput sequencing techniques to examine the effects of fecal microbiota transplants for patients diagnosed with C. difficile infections or pouchitis (an infectious state arising after a surgically-created pouch has been formed from ileal gut tissue as part of a treatment for ulcerative colitis or other diseases).